4YPI: Ebola virus nucleoprotein N-terminal fragment

Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35. Determined by X-ray diffraction at 3.71 Å resolution. Released 8 Apr 2015.

Method: X-ray diffraction
Resolution: 3.71 Å
Organism: Zaire ebolavirus (strain Mayinga-76)
Chains: 8
Atoms: 11,780
Mol. weight: 168.16 kDa
Released: 8 Apr 2015

Explore 4YPI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YPI contains 96 α-helices and 20 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	40-45	6	3
α-helix	49-62	14
α-helix	70-82	13
α-helix	87-92	6
α-helix	94-102	9
β-strand	105-110	6	3
α-helix	118-120	3
α-helix	127-136	10
α-helix	147-161	15
α-helix	165-182	18
α-helix	194-206	13
α-helix	209-219	11
α-helix	227-239	13
α-helix	245-254	10
β-strand	255-258	4	4
β-strand	261-264	4	4
α-helix	266-269	4
α-helix	271-273	3
α-helix	274-288	15
α-helix	291-296	6
α-helix	297-300	4
α-helix	304-307	4
α-helix	310-312	3
α-helix	314-327	14
α-helix	338-365	28
α-helix	370-383	14

Chain B: 22 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	40-45	6	5
α-helix	49-62	14
α-helix	70-82	13
α-helix	87-92	6
α-helix	94-102	9
β-strand	105-110	6	5
α-helix	118-120	3
α-helix	124-136	13
α-helix	147-161	15
α-helix	165-182	18
α-helix	194-206	13
α-helix	209-219	11
α-helix	227-239	13
α-helix	245-254	10
β-strand	255-258	4	6
β-strand	261-264	4	6
α-helix	266-269	4
α-helix	271-273	3
α-helix	274-288	15
α-helix	291-296	6
α-helix	297-300	4
α-helix	304-307	4
α-helix	310-312	3
α-helix	314-327	14
α-helix	338-365	28
α-helix	370-384	15

Chain C: 22 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	40-45	6	1
α-helix	49-62	14
α-helix	70-82	13
α-helix	87-92	6
α-helix	94-102	9
β-strand	105-110	6	1
α-helix	118-120	3
α-helix	127-136	10
α-helix	147-161	15
α-helix	165-182	18
α-helix	194-206	13
α-helix	209-219	11
α-helix	227-239	13
α-helix	245-254	10
β-strand	255-258	4	2
β-strand	261-264	4	2
α-helix	266-269	4
α-helix	271-273	3
α-helix	274-288	15
α-helix	291-296	6
α-helix	297-300	4
α-helix	304-307	4
α-helix	310-312	3
α-helix	314-327	14
α-helix	338-366	29
α-helix	370-384	15

Chain D: 22 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	40-45	6	7
α-helix	49-62	14
α-helix	70-82	13
α-helix	87-92	6
α-helix	94-102	9
β-strand	105-110	6	7
α-helix	118-120	3
α-helix	127-136	10
α-helix	147-161	15
α-helix	165-182	18
α-helix	194-206	13
α-helix	209-219	11
α-helix	227-239	13
α-helix	245-254	10
β-strand	255-258	4	8
β-strand	261-264	4	8
α-helix	266-269	4
α-helix	271-273	3
α-helix	274-288	15
α-helix	291-296	6
α-helix	297-300	4
α-helix	304-307	4
α-helix	310-312	3
α-helix	314-327	14
α-helix	338-365	28
α-helix	370-384	15

Chains E, F, G and H: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	22	1	4
α-helix	28-35	8
α-helix	40-42	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoprotein	A, B, C, D	protein	348	Zaire ebolavirus (strain Mayinga-76)	P18272 (AlphaFold model)
Polymerase cofactor VP35	E, F, G, H	protein	28	Zaire ebolavirus (strain Mayinga-76)	Q05127 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4YPI_1 Nucleoprotein (chains A, B, C, D)
QRVIPVYQVNNLEEICQLIIQAFEAGVDFQESADSFLLMLCLHHAYQGDYKLFLESGAVK
YLEGHGFRFEVKKRDGVKRLEELLPAVSSGKNIKRTLAAMPEEETTEANAGQFLSFASLF
LPKLVVGEKACLEKVQRQIQVHAEQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKFLLIHQ
GMHMVAGHDANDAVISNSVAQARFSGLLIVKTVLDHILQKTERGVRLHPLARTAKVKNEV
NSFKAALSSLAKHGEYAPFARLLNLSGVNNLEHGLFPQLSAIALGVATAHGSTLAGVNVG
EQYQQLREAATEAEKQLQQYAESRELDHLGLDDQEKKILMNFHQKKNE

Sequence of entity 2 (E, F, G, H), FASTA

>4YPI_2 Polymerase cofactor VP35 (chains E, F, G, H)
MPGPELSGWISEQLMTGRIPVSDIFCDI

Primary citation

An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions. Leung, D.W., Borek, D., Luthra, P. et al. Cell Rep (2015) 11:376-389. DOI 10.1016/j.celrep.2015.03.034 · PubMed

Other PDB entries of the same protein (UniProt P18272 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QB0 1.75 Å, The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein
4Z9P 1.79 Å, Crystal structure of Ebola virus nucleoprotein core domain at 1.8A resolution
4QAZ 1.98 Å, The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein
5T3T 2.2 Å, Ebola virus VP30 CTD bound to nucleoprotein
4ZTA 2.4 Å, Ebola virus nucleoprotein bound to VP35 chaperoning peptide I212121
4ZTI 2.4 Å, Ebola virus nucleoprotein bound to VP35 chaperoning peptide P212121
4ZTG 2.8 Å, Ebola virus nucleoprotein bound to VP35 chaperoning peptide P22121
6NUT 3.1 Å, Ebola virus nucleoprotein - RNA complex
5Z9W 3.6 Å, Ebola virus nucleoprotein-RNA complex
8Y9J 4.6 Å, Structure of the Ebola virus nucleocapsid subunit
6C54 5.8 Å, Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit
6EHL 6.6 Å, Model of the Ebola virus nucleoprotein in recombinant nucleocapsid-like assemblies

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